Premachandra H K A, Piza-Roca Carme, Casteriano Andrea, Higgins Damien P, Hohwieler Katrin, Powell Daniel, Cristescu Romane H
University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, QLD, 4556, Australia.
Faculty of Science/ Sydney School of Veterinary Science, University of Sydney, NSW, 2006, Camperdown, Australia.
Sci Rep. 2024 Dec 5;14(1):30371. doi: 10.1038/s41598-024-76873-1.
Wildlife diseases are major players in local and global extinctions. Effective disease surveillance, management and conservation strategies require accurate estimates of pathogen prevalence. Yet pathogen detection in wild animals remains challenging. Current gold standards often require samples collected through veterinary examination, but this method is costly, intensive, invasive, and requires specialised staff and equipment. Collection of non-invasive samples, such as scats, is an effective monitoring tool which can be deployed at large scale, as scats contain DNA of both host and pathogens. The koala (Phascolarctos cinereus) is listed as 'endangered' under the EPBC Act 1999, with chlamydial disease representing a major threat. Here, we present a new approach that combines restriction-enzyme associated sequencing and targeted-sequence-capture genotyping, namely DArTcap, to detect Chlamydia pecorum in koala scats. We found this method has similar accuracy to current gold standards (qPCR of swab samples), with a sensitivity of 91.7% and a specificity of 100%. This method can be incorporated into existing koala genetic studies using marker panels, where population attributes can be estimated alongside C. pecorum presence, using the same scat samples, with the option to add further markers of interest. Such a one-stop-shop panel would considerably reduce processing times and cost.
野生动物疾病是导致局部和全球物种灭绝的主要因素。有效的疾病监测、管理和保护策略需要准确估计病原体的流行率。然而，在野生动物中检测病原体仍然具有挑战性。目前的金标准通常需要通过兽医检查采集样本，但这种方法成本高、强度大、具有侵入性，并且需要专业人员和设备。采集非侵入性样本，如粪便，是一种有效的监测工具，可以大规模部署，因为粪便中含有宿主和病原体的DNA。考拉（Phascolarctos cinereus）在1999年《环境保护和生物多样性保护法》中被列为“濒危”物种，衣原体疾病是其面临的主要威胁。在此，我们提出一种新方法，将限制性内切酶相关测序和靶向序列捕获基因分型相结合，即DArTcap，用于检测考拉粪便中的考拉衣原体。我们发现这种方法与当前的金标准（拭子样本的qPCR）具有相似的准确性，灵敏度为91.7%，特异性为100%。这种方法可以纳入现有的使用标记面板的考拉基因研究中，在这些研究中，可以使用相同的粪便样本，在估计考拉衣原体存在的同时估计种群属性，并且可以选择添加其他感兴趣的标记。这样一个一站式面板将大大减少处理时间和成本。
